Just recently my 1.9 TDI is difficult to start first thing in the morning, when it does start runs rough for a few seconds then o.k. all day,

I have replaced glow plugs (tested old ones they were o.k.) could it be coolant temp sender? not sending correct message to ECU as some times guage drops to zero then will return to normal/90

thanks

It could be the CTS - can you get vagcom on the car to check the outputs (and to check for fault codes)?